'Breakthrough Articles’ present high-impact studies answering long-standing questions in the field of nucleic acids research and/or opening up new areas and mechanistic hypotheses for investigation. These articles are chosen by the Editors on the recommendation of Editorial Board Members and Referees. Articles are accompanied by a brief synopsis explaining the findings of the paper and where they fit in the broader context of nucleic acids research. Breakthrough Articles replace the older 'Featured Articles’, which have been discontinued. They represent the very best papers published at NAR.
Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure
Grand RS, Pichugina T, Gehlen LR, Jones MB, Tsai P, Allison JR, Martienssen R, O'Sullivan JM.
In this work, Grand, O'Sullivan and co-workers capture the structure of the Schizosaccharomyces pombe genome and the transcriptome at different stages of the cell cycle. The authors find that the interactions between genes correlates with their transcriptional activity at specific stages of the cell cycle. In silico modelling of the genome suggests that genes that are highly expressed at all stages of the cell cycle are located towards the centre of the nucleus. Conversely, genes that are differentially expressed tend to be located towards the periphery of the nucleus. Based on these findings the authors conclude that the S. pombe nucleus is spatially divided into functional sub-nuclear domains that correlate with gene activity.
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Paramecium tetraurelia chromatin assembly factor-1-like protein PtCAF-1 is involved in RNA-mediated control of DNA elimination
Ignarski M, Singh A, Swart EC, Arambasic M, Sandoval PY, Nowacki M.
CAF-1 protein is a histone chaperone that is involved in the deposition of nucleosomes on newly replicated DNA and in the regulation of gene expression. In addition, defects of CAF-1 have been detected in various types of cancers. This study identifies a new role for CAF-1, based on findings in a laboratory model organism, the ciliated protozoan, Paramecium tetraurelia. A CAF-1 homolog in this organism facilitates the process of RNA-mediated programming of genome rearrangements. It enables selection of parental small RNAs that shape the genome of progeny cells during development. The research opens up new directions for studies of RNA-mediated maintenance of genome stability, eukaryotic chromosomal rearrangements, and perhaps DNA repair. Free Full Text
Mechanism of retinoic acid-induced transcription: histone code, DNA oxidation and formation of chromatin loops
Zuchegna C, Aceto F, Bertoni A, Romano A, Perillo B, Laccetti P, Gottesman ME, Avvedimento EV, Porcellini A.
Many eukaryotic genes are activated as a result of the interaction between nuclear receptors, or 'NRs' (which binding a wide variety of small molecules, such as thyroid hormones, that are important for transcriptional activation), their ligands, and DNA promoter regions. There are many reports on the modifications of chromatin and accumulation of NR-induced mRNAs of specific genes , but to date a mechanism that links activated receptor to the transcription of specific genes is still unclear. This paper provides evidence that transcriptional activation by one particular type of NR (the retinoic acid, or 'RA' receptor) involved a sequential wave of histone methylation changes, DNA oxidation and corresponding recruitment of DNA repair enzymes, formation of localized chromatin loops, and finally activation of the polymerase complex, resulting in the generation of RA-induced mRNAs. These early transcription activation event has been named the “non-productive transcription cycle”, and are believed to characterize the earliest stages of transcription induction by nuclear receptors. Free Full Text
Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli
Clarke JE, Kime L, Romero AD, McDowall KJ.
This paper indicates that a major factor in defining the transcriptional landscapes of E. coli, and probably the large number of organisms that contain orthologues of RNase E, is ‘direct entry’ cleavage. It dispels the notion that the only common mechanism by which RNase E cleaves RNA requires interaction with a 5'-monophosphorylated end. Moreover, further evidence is presented that direct entry is facilitated by RNase E binding simultaneously to two or possibly more unpaired regions. These simple requirements may maximise the rate of degradation and processing by permitting multiple sites in a transcript to be surveyed directly without being constrained by 5′-end tethering. The specificity of RNase E is sufficiently flexible that it can cleave at some sites using different combinations of unpaired regions. Discussion within the paper includes the evolution of 5’ sensing, one of the hallmarks of the RNase E family, the role of the RNA degradosome and possible new roles for RNase E. Free Full Text
Structural basis of lariat RNA recognition by the intron debranching enzyme Dbr1
Montemayor EJ, Katolik A, Clark NE, Taylor AB, Schuermann JP, Combs DJ, Johnsson R, Holloway SP, Stevens SW, Damha MJ, Hart PJ.
Crystal structures of an intron debranchilay summery gku808ng enzyme (Dbr1) are determined alone and in complex with several synthetic RNA compounds that mimic the branchpoint in lariat RNA. Together with functional data, the structures reveal the molecular basis for branched RNA recognition and explain why the enzyme lacks activity towards 3',5'-phosphodiester linkages. Dbr1 is the only enzyme known to hydrolyze the 2',5'-phosphodiester bond in lariat RNA. Hydrolysis of this bond is required before spliced introns can be metabolized or processed into essential snoRNA and miRNA. These are the first Dbr1 structures to be reported. Free Full Text
7SL RNA represses p53 translation by competing with HuR
Abdelmohsen K, Panda AC, Kang MJ, Guo R, Kim J, Grammatikakis I, Yoon JH, Dudekula DB, Noh JH, Yang X, Martindale JL, Gorospe M.
A major goal of cancer biology is to identify useful therapeutic targets. Noncoding (nc)RNAs have emerged as key gene regulators in many pathologies, including cancer. Here the authors report that the ncRNA 7SL is more abundant in cancer tissues than in normal tissues. 7SL forms RNA hybrids with TP53 mRNA, which encodes p53 (one of the tumor suppressors most often lost in cancer), and represses p53 translation. These findings uncover 7SL as the first ncRNA that binds and represses TP53 mRNA translation, and suggest that targeting 7SL may be effective in the treatment of cancers with reduced p53 levels. Free Full Text
A dimeric state for PRC2
Davidovich C, Goodrich KJ, Gooding AR, Cech TR.
Polycomb repressive complex-2 (PRC2) is a histone methyltransferase required for epigenetic silencing during development and cancer. Here we provide the first direct evidence, using multiple independent approaches, that the four-subunit and five-subunit PRC2 complexes are dimers, including eight and ten protein subunits, respectively. We are further showing that each PRC2 dimer binds a single RNA, but a single RNA can bind multiple PRC2 dimers. Our findings lead to a new molecular mechanism that can explain how a single RNA transcript can nucleate repression by binding multiple PRC2 complexes, through PRC2 dimerization and cooperative RNA binding. Free Full Text
Targeted delivery of antisense oligonucleotides to hepatocytes using triantennary N-acetyl galactosamine improves potency 10-fold in mice
Prakash TP, Graham MJ, Yu J, Carty R, Low A, Chappell A, Schmidt K, Zhao C, Aghajan M, Murray HF, Riney S, Booten SL, Murray SF, Gaus H, Crosby J, Lima WF, Guo S, Monia BP, Swayze EE, Seth PP.
Inefficient delivery of antisense oligonucleotides to target tissues can limit the efficacy of nucleic acid drugs. The authors demonstrate that a GalNac modification can enhance the potency and duration of action of two different antisense oligonucleotides targeting important biomedical targets human apolipoprotein C-III and transthyretin. The relatively straightforward chemical modification revealed in this paper improves potency by approximately 10-fold. By reducing the amount of drug needed cost will be lowered and the potential for side effects probably reduced. While the GalNac conjugates will only improve potency in the liver, one can imagine using similar modification strategies to assist uptake by other organs. The liver is already a focus for antisense therapy, so there is likely to be a significant impact on clinical development in the near term. Free Full Text
PARP-2 and PARP-3 are selectively activated by 5′ phosphorylated DNA breaks through an allosteric regulatory mechanism shared with PARP-1
Langelier MF, Riccio AA, Pascal JM.
This paper describes details of a mechanism by which two DNA damage-dependent enzymes (termed 'Poly-ADP-ribose polymerases' or 'PARPs') respond to DNA damage, through specific activation in response to generation of free 5' phosphate groups at the sites of DNA strand breaks. The study demonstrated that two PARP family members (PARP-2 and PARP-3) may exploit these interactions to act at late stages of the repair process for such strand breaks, perhaps by facilitating subsequent ligation of the cleaved DNA ends. These results provide new insight into mechanisms by which the fidelity of a genome (which is under constant assault by a wide variety of internal and external DNA damaging agents in the cell) is maintained through the action of protective repair molecules. Free Full Text
Critical role for p53-serine 15 phosphorylation in stimulating transactivation at p53-responsive promoters
Loughery J, Cox M, Smith LM, Meek DW.
This study focuses on a key aspect of the mechanism by which the p53 tumour suppressor protein, which is crucial in preventing cancer cell survival, is activated upon receiving an appropriate stimulus. The authors show that a specific reversible chemical modification of p53 (phosphorylation) previously thought to have a limited involvement, is essential for p53 function and is required for the ability of p53 to activate the cellular machinery that leads to the manufacture of the cellular components needed to combat cancer-associated changes in the cell. This information extends our knowledge of the basic principles by which p53 functions and is controlled. Free Full Text
HIV-1 Rev protein specifies the viral RNA export pathway by suppressing TAP/NXF1 recruitment
Taniguchi I, Mabuchi N, Ohno M.
These studies address a long standing question about the export of HIV-1 RNAs, establish a previously unrecognized function of the viral Rev protein and in so doing suggest potential new targets for anti-retroviral drugs. Free Full Text
Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification
Neumann P, Lakomek K, Naumann PT, Erwin WM, Lauhon CT, Ficner R.
More than 100 chemically modified nucleosides have been identified in tRNAs. One of them, 4-thiouridine, is found at position 8 of all tRNAs in bacteria and archaea. It stabilizes the tRNA fold and, in addition, serves as UV light sensor inducing a cellular response to UV radiation. The structural basis for the exclusive C4-thiolation of U8 has been elucidated by the crystal structure analysis of a 4-thiouridine synthetase - RNA complex. The structure revealed that the enzyme employs a molecular ruler measuring the distance from the 3’-CCA end, which is common to all tRNAs, to the site of modification. Free Full Text
Structure of human RNA N6-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation
Aik W, Scotti JS, Choi H, Gong L, Demetriades M, Schofield CJ, McDonough MA.
It is now widely recognised that nucleic acids can be marked with chemical groups, or ‘tagged’, in the form of methylation. Like an accented letter of the alphabet (e.g. á), these marks change the way the genetic code is ‘read’, resulting in a change in gene expression. Enzymes that tag nucleic acids with methyl-mark 'accents' are called methyltransferases and can be thought of as ‘writers’. Enzymes that remove methyl-mark accents are called demethylases or ‘erasers’. This dynamic nucleic acid modification process provides for a complex regulatory mechanism of gene expression known as epigenetics. ALKBH5 is one of two enzymes known to ‘erase’ N6-methyladenine (m6A) on RNA. Recently discovered cellular and physiological roles (e.g. obesity, fertility and circadian rhythm) for RNA m6A have been exciting researchers in all aspects of biology. The crystal structure presented here reveals the mechanisms of nucleic acid recognition and demethylation of ALKBH5, laying a foundation for further mutational and inhibition studies. Free Full Text
Three-tiered role of the pioneer factor GATA2 in promoting androgen-dependent gene expression in prostate cancer
Wu D, Sunkel B, Chen Z, Liu X, Ye Z, Li Q, Grenade C, Ke J, Zhang C, Chen H, Nephew KP, Huang TH, Liu Z, Jin VX, Wang Q.
Though the importance of GATA family pioneer factors in facilitating ligand-inducible nuclear receptor activity is well appreciated, the mechanism of their action is not fully understood. We show in prostate cancer cells, in which disease-related gene expression is stimulated by male hormones acting through the androgen receptor (AR), that GATA2 takes a three-pronged approach in advance of hormone treatment to prime for AR-driven gene expression. Our findings establish a hormone-independent role for GATA2 in determining chromatin accessibility of gene regulatory elements and as a component of transcription-activating chromatin loops within AR target gene loci. Free Full Text
A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis
Pimentel H, Parra M, Gee S, Ghanem D, An X, Li J, Mohandas N, Pachter L, Conboy JG.
By comparing alternative pre-mRNA splicing in five morphologically distinct populations of successively more differentiated erythroblasts, the authors characterized a robust and dynamic erythroid alternative pre-mRNA splicing program. Erythroblast alternative splicing is particularly enriched in genes controlling cell cycle, organelle organization, chromatin function, and RNA processing. Differentiation stage-specific changes in splicing are executed in concert with, and may help drive, major cellular remodeling in the last stages before enucleation. A subset of splicing switches introduce premature translation termination codons, indicating that alternative splicing-coupled nonsense-mediated-decay (AS-NMD) contributes to regulation of erythroid-expressed genes as a novel part of the overall differentiation program. Free Full Text
The Vertebrate Genome Annotation browser 10 years on
Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE, Mudge J, Sheppard D, Thomas M, Trevanion S, Wilming LG.
The Vertebrate Genome Annotation (VEGA) browser is a database for viewing manually curated genes on high quality genome sequence. It has recently been updated with an improved user interface to make navigating the different datasets easier. We have increased the number of annotated genomes to include human, mouse, zebrafish, rat and pig whole genomes, plus small regions of medical interest from organisms as diverse as gorilla, wallaby and Tasmanian devil. Free Full Text
TFBSshape: a motif database for DNA shape features of transcription factor binding sites
Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gordân R, Rohs R.
Our current understanding of DNA binding specificities of transcription factors (TFs) mainly results from nucleotide sequence analysis. However, proteins recognize DNA as a three-dimensional object. Thus, an improved comprehension of DNA binding specificity must be based on DNA structure. The TFBSshape database augments nucleotide sequence motifs with heat maps and quantitative predictions of DNA shape features for 739 TF datasets from 23 different species. Sequence information analyzed by TFBSshape is collected from the motif databases JASPAR and UniPROBE. The structural characterization of transcription factor binding sites (TFBSs) can aid users in gaining further insights into the mechanisms underlying TF-DNA recognition. Free Full Text
Cycling of the E. coli lagging strand polymerase is triggered exclusively by the availability of a new primer at the replication fork
Yuan Q, McHenry CS.
Two models have been proposed for triggering release of the lagging strand polymerase at the E. coli replication fork, enabling cycling to the primer for the next Okazaki fragment—either collision with the 5’-end of the preceding fragment (collision model), or synthesis of a new primer (signaling model). Specific perturbation of lagging strand elongation on minicircles confirmed the signaling model and ruled out the collision model. It was demonstrated that the presence of a primer, not primase per se, provides the cycling signal and that the rate of lagging strand elongation is faster than the leading strand. Free Full Text
The double PHD finger domain of MOZ/MYST3 induces α-helical structure of the histone H3 tail to facilitate acetylation and methylation sampling and modification
Dreveny I, Deeves SE, Fulton J, Yue B, Messmer M, Bhattacharya A, Collins HM, Heery DM.
New crystal structures reveal for the first time that the Double PHD Finger domain of the chromatin regulator MOZ/MYST3 can induce an alpha helical fold of the N-terminal tail of Histone H3. This enables MOZ to sample for the presence of existing histone modifications, and promotes acetylation of H3K14 by the MYST domain. A conserved double glycine hinge motif in the H3 tail is essential to allow the acetylated H3K14 residue to dock with the DPF domain. The study provides important new insights into how a chromatin regulator manipulates and modifies histone tail structure to dictate its own residency on chromatin. Free Full Text
Co-regulated gene expression by estrogen receptor-α and liver receptor homolog-1 is a feature of the estrogen response in breast cancer cells
Lai CF, Flach KD, Alexi X, Fox SP, Ottaviani S, Thiruchelvam PT, Kyle FJ, Thomas RS, Launchbury R, Hua H, Callaghan HB, Carroll JS, Charles Coombes R, Zwart W, Buluwela L, Ali S.
Most breast cancers are estrogen responsive and require the Estrogen receptor-α (ERα) transcription factor. By mapping DNA binding in the genome of breast cancer cells, we show that a distantly related transcription factor, LRH-1, co-regulates target genes with ERα, through the use of overlapping DNA binding motifs. Remarkably, LRH-1 promotes changes in chromatin to facilitate ERα recruitment, thereby leading to a co-operative regulation of gene expression. These findings provide evidence for a novel mechanism of gene regulation, whereby the binding of one transcription factor promotes the subsequent recruitment of another transcription factor to the same binding site. Free Full Text
Pre-activation of the genome integrity checkpoint increases DNA damage tolerance
Tsaponina O, Chabes A.
The genome integrity checkpoint monitors and reacts to defects in the genome, and it is well known that mutations in genes involved in this pathway cause sensitivity to DNA-damaging agents. Here, using budding yeast, we show that a low level of constitutive genome integrity checkpoint activation by hydroxyurea, an inhibitor of DNA replication, can increase DNA damage tolerance to multiple drugs, some of which are commonly used for cancer treatment. Modulation of the checkpoint activity may provide new strategies for utilizing this checkpoint to protect normal cells from genotoxic stress. Free Full Text
Promoter RNA Links Regulation of Inflammatory Pathways Genes
Matsui M, Chu Y, Zhang H, Gagnon KT, Shaikh S, Kuchimanchi S, Manoharan M, Corey DR, Janowski BA.
This manuscript lays out a new mechanism for using RNA to sequence-specifically recruit proteins and modulate transcription in mammalian cells. Free Full Text
Increasing The Complexity Of Chromatin: Functionally Distinct Roles For Replication-Dependent Histone H2A Isoforms In Cell Proliferation And Carcinogenesis
Singh R, Mortazavi A, Telu KH, Nagarajan P, Lucas DM, Thomas-Ahner JM, Clinton SK, Byrd JC, Freitas MA, Parthun MR.
Complexity is a critical characteristic of chromatin structure that allows for the myriad regulatory mechanisms that control cellular phenomena involving genomic DNA. The complexity of chromatin is currently thought to derive from the abundance of histone post-translational modifications and the presence of DNA replication-independent histone variants, such as histone H3.3, and histone H2AZ. Our manuscript identifies a source of complexity that has gone unexplored; replication-dependent histone isoforms. Free Full Text
Helq acts in parallel to Fancc to suppress replication-associated genome instability
Luebben SW, Kawabata T, Akre MK, Lee WL, Johnson CS, O'Sullivan MG, Shima N.
HELQ is a DNA repair enzyme that has been implicated in the Fanconi anemia (FA) pathway, a major mechanism to repair a specific type of lesion called DNA interstrand crosslinks (ICLs). Using the first reported Helq mutant mouse model, the authors show that HELQ plays only a minor role in ICL repair. Rather, HELQ was found to function in parallel to the FA core complex member FANCC for the successful completion of DNA replication and the promotion of genome integrity. This newly identified role of HELQ provides new insights into the etiology of FA, a human genetic disorder. Free Full Text
Attachment site recognition and regulation of directionality by the serine integrases
Rutherford K, Yuan P, Perry K, Sharp R, Van Duyne GD.
A family of enzymes known as the serine integrases are able to rearrange DNA molecules in the test tube, in cultured cells, and in live animals. They are particularly effective at delivering a new DNA sequence into a specific site in a chromosome, a process that has important implications for gene therapy and a variety of genetic engineering applications. This manuscript explain how serine integrases carry out these complex reactions, provides a plausible mechanism for their unidirectionality, and provide a much needed experimental framework for improving the properties and altering specificities in these systems. Free Full Text
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